TY  - GEN
N2  - Despite decades of conventional chemotherapy, the prognosis for patients with acute myeloid leukemia (AML) remains dismal, with 75% of patients succumbing to their disease within 5 years of diagnosis. Recent advances in cancer therapy have turned to the immune system for specific targeting and clearance of tumors. However, to date, there is not a comprehensive understanding of the neoepitope landscape in AML that could be used in the next generation of immunotherapies. In this study, genomic data from 562 patients (cohort: Beat AML program, Oregon Health & Science University) were analyzed computationally to identify tumor variants, altered mRNA sequences of variants, and HLA-type. Using a computational pipeline and algorithm (neoepiscope), we were able to predict 8-11 amino acid peptide sequences (aka: epitopes) from DNA-seq of complementary tumor and normal patient samples which consider germline context and the potential for co-occurrence of two or more somatic variants on the same mRNA transcript.
DO  - 10.6083/h989r4099
DO  - DOI
AB  - Despite decades of conventional chemotherapy, the prognosis for patients with acute myeloid leukemia (AML) remains dismal, with 75% of patients succumbing to their disease within 5 years of diagnosis. Recent advances in cancer therapy have turned to the immune system for specific targeting and clearance of tumors. However, to date, there is not a comprehensive understanding of the neoepitope landscape in AML that could be used in the next generation of immunotherapies. In this study, genomic data from 562 patients (cohort: Beat AML program, Oregon Health & Science University) were analyzed computationally to identify tumor variants, altered mRNA sequences of variants, and HLA-type. Using a computational pipeline and algorithm (neoepiscope), we were able to predict 8-11 amino acid peptide sequences (aka: epitopes) from DNA-seq of complementary tumor and normal patient samples which consider germline context and the potential for co-occurrence of two or more somatic variants on the same mRNA transcript.
AD  - Oregon Health and Science University
T1  - In silico assessment of somatic mutation generated T cell epitopes in various subsets of acute myeloid leukemia
DA  - 2021
AU  - Loo, Christopher P.
L1  - https://digitalcollections.ohsu.edu/record/9295/files/Loo.Christopher.2021.pdf
PB  - Oregon Health & Science University
PY  - 2021
ID  - 9295
L4  - https://digitalcollections.ohsu.edu/record/9295/files/Loo.Christopher.2021.pdf
KW  - Computational Biology
KW  - bioinformatics
KW  - cancer
KW  - immunology
TI  - In silico assessment of somatic mutation generated T cell epitopes in various subsets of acute myeloid leukemia
Y1  - 2021
L2  - https://digitalcollections.ohsu.edu/record/9295/files/Loo.Christopher.2021.pdf
LK  - https://digitalcollections.ohsu.edu/record/9295/files/Loo.Christopher.2021.pdf
UR  - https://digitalcollections.ohsu.edu/record/9295/files/Loo.Christopher.2021.pdf
ER  -